GEO series

Bronchoalveolar lavage of healthy human adults after LPS exposure

GSE300946 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2025/08/14 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 15 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 15 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Simulating paired and longitudinal single-cell RNA sequencing data with rescueSimBioinformatics (Oxford, England) · 2025

Summary (written by the submitters)

Rationale: Macrophages are both drivers of dysregulated inflammation and essential for healthy repair following acute lung injury. Distinct subsets of human macrophages have been associated with lung pathology but whether unique cellular programs are causally linked to disease or merely represent a conserved response to tissue damage is unknown.

Read the full summary ↓

Objectives: We sought to identify the transcriptional heterogeneity and cellular programing of airspace macrophages (AM) during normal lung repair in a human model of self-resolving acute lung injury. Methods: Fifteen subjects underwent bronchoscopic lavage before and at a pre-assigned time point after endobronchial exposure to bacterial endotoxin. Cells from lavage were subjected to single-cell RNA sequencing and a longitudinal assessment of AM programing during resolution of inflammation and lung repair was performed. Measurements and Main Results: We identify transcriptionally distinct subsets of AM present at all time points, in all subjects. We focus on two populations that increase following inflammation, one which aligns closely with classical circulating monocytes (MoAM) and one with interstitial macrophages (IMAM). Comparison of subset-specific markers to those identified in disease states reveals that IMAM express many so-called “pathogenic” macrophage markers during both health and inflammation. Conclusions: By applying a uniform inflammatory stimulus to healthy adults and examining BAL cells obtained at precise time points following inflammation, we construct a time-resolved kinetic of AM transcriptional programing during inflammation and normal lung repair. Our data suggest that IMAM are similar to cells identified at increased frequency in disease states and may reflect a conserved cellular response to tissue injury.

Published in

Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim

Wynn EA, Mould KJ, Vestal BE et al. · Bioinformatics (Oxford, England) 2025 · PMID 40811017 · doi:10.1093/bioinformatics/btaf442

This dataset

Open GSE300946 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300946_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1282722 and SRA study SRP595011. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40811017) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 15 more — browse all 15 samples with per-sample file links →

Datasets on a similar topic

GSE309422 RNAseq analysis of human neutrophil mRNA from adults with SLE and age-matched healthy controls 21 samples shares healthy, adults
GSE217516 Single-cell RNA-sequencing of bronchoalveolar lavage cells from humans with bronchiectasis 6 samples shares bronchoalveolar, lavage
GSE263448 Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells 46 samples shares bronchoalveolar, lavage
GSE296682 Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease 9 samples shares bronchoalveolar, lavage
GSE184487 RNA-sequencing of PBMC cultured with PolyI:C or LPS, from a pediatric cohort who received OM85 or placebo. 193 samples shares lps
GSE328566 LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages 24 samples shares lps
GSE327840 RNA-seq profiling of LPS tolerance in monocytes, THP-1, fibroblasts, smooth muscle cells, and endothelial cells 58 samples shares lps
GSE317449 Effect of depletion of TSPAN6 on Biliary Epithelial Cells with and without LPS stimulation mirroring liver disease. 20 samples shares lps

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.